27228c7e494674469a64cdeb61d7c4e433102f24
hiram
Thu Jan 2 13:16:14 2020 -0800
updated text to global reference wording refs #24534
diff --git src/hg/makeDb/doc/globalReference/mkAsmStats.pl src/hg/makeDb/doc/globalReference/mkAsmStats.pl
index 8d0ce11..86bdb9f 100755
--- src/hg/makeDb/doc/globalReference/mkAsmStats.pl
+++ src/hg/makeDb/doc/globalReference/mkAsmStats.pl
@@ -1,270 +1,272 @@
#!/usr/bin/env perl
use strict;
use warnings;
use File::stat;
my $asmHubWorkDir = "globalReference";
my @orderList; # asmId of the assemblies in order from the *.list files
# the order to read the different .list files:
my @classList = qw( human );
my %class; # key is asmId, value is from class list
my $assemblyCount = 0;
my $overallNucleotides = 0;
my $overallSeqCount = 0;
my $overallGapSize = 0;
my $overallGapCount = 0;
my %ethnicGroup; # ksy is asmId, value is ethnicity
my %countryOfOrigin; # ksy is asmId, value is country of origin
##############################################################################
# from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters:
##############################################################################
sub commify($) {
my $text = reverse $_[0];
$text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;
return scalar reverse $text
}
##############################################################################
### start the HTML output
##############################################################################
sub startHtml() {
my $timeStamp = `date "+%F"`;
chomp $timeStamp;
print <<"END"
-
+
-Platinum Genomes Project assembly statistics
+Global Reference Genomes Project assembly statistics
-This assembly hub contains assemblies released
-by the
-Platinum Genomes Project.
-
+This assembly hub contains assemblies collected by the
+Reference
+Genome Improvement Project from Washington University in Saint Louis, Missouri, USA. For more
+information, contact
+
+Tina Graves-Lindsay.
Data resource links
NOTE: Click on the column headers to sort the table by that column
END
}
##############################################################################
### start the table output
##############################################################################
sub startTable() {
print <<"END"
| count | ethnicity
link to genome browser |
country of origin
and data download |
NCBI assembly |
sequence
count | genome size
nucleotides |
gap
count | unknown bases
(gap size sum) | masking
percent |
|---|
END
}
##############################################################################
### end the table output
##############################################################################
sub endTable() {
my $commaNuc = commify($overallNucleotides);
my $commaSeqCount = commify($overallSeqCount);
my $commaGapSize = commify($overallGapSize);
my $commaGapCount = commify($overallGapCount);
print <<"END"
| TOTALS: | assembly count $assemblyCount |
$commaSeqCount |
$commaNuc |
$commaGapCount |
$commaGapSize |
|
|---|
END
}
##############################################################################
### end the HTML output
##############################################################################
sub endHtml() {
print <<"END"